Most frequently mutated genes in VCF

Question

[Ron]

Hi all,

I am doing mutation analysis from RNAseq data and I have a VCF file. I want to get most frequently mutated genes(most number of mutations per gene) from the VCF file,and used snpEFF

count number of variants per gene from .vcf annovar&snpsift

However I dont think this is the output what I need.Please see the output below:

chr start   end type    IDs Reads:ALLMUT_FILTERED_Annotated
1   1   11873   Intergenic;DDX11L1  1   1
1   1   11873   Intergenic;DDX11L1  1   1
1   1   249250621   Chromosome;1    638541  638541
1   6874    11873   Upstream;NR_046018.2;;DDX11L1;Non-coding_transcript 1   1
1   6874    11873   Upstream;NR_046018.2;;DDX11L1;Non-coding_transcript 1   1
1   9362    14361   Downstream;NR_024540.1;;WASH7P;Non-coding_transcript    7   7
1   9362    14361   Downstream;NR_024540.1;;WASH7P;Non-coding_transcript    7   7
1   11874   14409   Gene;DDX11L1;Non-coding_transcript  6   6
1   11874   14409   Transcript;NR_046018.2;;DDX11L1;Non-coding_transcript   6   6
1   12369   17368   Downstream;NR_106918.1.3;;MIR6859-1.3;Non-coding_transcript 170 170
1   12369   17368   Downstream;NR_106918.1.3;;MIR6859-1.3;Non-coding_transcript 170 170
1   12369   17368   Downstream;NR_107062.1.2;;MIR6859-2.2;Non-coding_transcript 170 170
1   12369   17368   Downstream;NR_107062.1.2;;MIR6859-2.2;Non-coding_transcript 170 170
1   12722   13220   Intron;intron_2_RETAINED-RETAINED;NR_046018.2;;DDX11L1;Non-coding_transcript    1   1
1   13221   14409   Exon;exon_3_3_RETAINED;NR_046018.2;;DDX11L1;Non-coding_transcript   5   5
1   14362   14829   Exon;exon_11_11_RETAINED;NR_024540.1;;WASH7P;Non-coding_transcript  74  74
1   14362   29370   Transcript;NR_024540.1;;WASH7P;Non-coding_transcript    361 361
1   14362   29370   Gene;WASH7P;Non-coding_transcript   361 361
1   14410   19409   Downstream;NR_046018.2;;DDX11L1;Non-coding_transcript   233 233
1   14410   19409   Downstream;NR_046018.2;;DDX11L1;Non-coding_transcript   233 233

Let me know if there is any way to do that,or I can just the count the mutations per gene by writing a script?

Thanks,

Ron

Answer 1

[Ram]

Check out -freq in vcftools.